fix(ase): symmetrize reshaped virial stress

[njzjz]

Summary

• reshape the nine-component model virial before transposing it
• project the virial onto ASE's symmetric Cauchy stress convention
• preserve the original, potentially asymmetric virial matrix in results["virial"]
• add a backend-independent mock regression with independently observable shear components

Root cause and fix

The calculator stored v[0].reshape(3, 3) as the virial, but formed stress from:

v[0].copy() + v[0].copy().T

v[0] is one-dimensional with shape (9,), and transposing a one-dimensional NumPy array is a no-op. The calculation therefore selected only one side of each off-diagonal pair when converting to ASE Voigt order.

The code now names the reshaped 3 x 3 virial, preserves it unchanged in the results dictionary, and computes:

-0.5 * (virial + virial.T) / volume

This matches ASE's symmetric stress convention and retains tensile-positive sign handling. It does not hide the original virial: callers can still inspect any antisymmetric component through results["virial"].

Why existing tests missed this

Standard conservative DeePMD models normally return a total virial that is already symmetric up to floating-point noise. Existing calculator integration tests use such real model output and mainly check permutation consistency, so the ineffective transpose was numerically invisible.

The new lightweight regression mocks the model with the intentionally asymmetric virial:

[[1, 2, 3],
 [4, 5, 6],
 [7, 8, 9]]

For volume 8, the correct ASE Voigt shear entries are based on averages yz=7, xz=5, and xy=3. The previous implementation deterministically returned the single-sided values 6, 3, and 2; the fixed implementation returns the expected symmetric values and leaves the stored virial unchanged.

Validation

• old calculation reproduced the incorrect deterministic shear values
• new backend-independent regression: passed
• existing PyTorch calculator tests: 2 passed
• independent review found no sign, Voigt-order, PBC, or backend-coupling issues
• ruff format --check .
• ruff check .
• git diff --check

Closes #5689.

Coding agent: Codex
Codex version: codex-cli 0.144.1
Model: gpt-5.6-sol
Reasoning effort: xhigh

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📥 Commits

Reviewing files that changed from the base of the PR and between 3122138 and 0486337.

📒 Files selected for processing (2)

• deepmd/calculator.py
• source/tests/test_calculator.py

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• Create PR with unit tests

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